Since coming from CuteFTP Pro, the one feature that I miss from CuteFTP is the ability to select/highlight multiple sites in my Site Manager and press Connect, which would then open all the connections to the selected sites all at once. This is much better than having open each site one at a time which is the current user experience within FileZilla.
This is especially useful when I have to upload the same files to multiple mirrored servers.
Hope this is a low hanging fruit type of feature request that would add some effective value ;)